Contacts of the helix formed by residues 304 - 313 (chain H) in PDB entry 1F1H
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 304 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300H GLY* 3.0 23.3 + - - +
301H VAL 3.6 2.5 - - - -
303H LYS* 1.3 102.4 + - + +
305H ALA* 1.3 64.8 + - - +
306H LYS 3.4 1.8 - - - -
307H ALA* 3.1 6.1 + - - +
308H ILE* 2.9 21.3 + - - +
377H ALA* 4.0 13.9 - - + -
380H ASP* 2.9 29.4 + - - -
386H ILE* 5.1 0.2 - - - +
424H ASP* 2.7 40.8 + - - +
427H PHE* 3.6 44.0 - + + +
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Residues in contact with ALA 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301H VAL 2.8 18.6 + - - +
302H ILE* 3.7 2.0 - - - +
303H LYS 3.4 3.0 + - - -
304H HIS* 1.3 73.9 - - - +
306H LYS* 1.3 58.5 + - - +
308H ILE* 2.8 11.8 + - - +
309H ASN* 2.8 35.9 + - - +
332H LEU* 3.6 43.1 - - + -
360H PHE* 4.6 11.2 - - + -
410H VAL* 5.1 0.9 - - + -
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Residues in contact with LYS 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303H LYS 5.2 1.0 + - - -
304H HIS 3.4 0.8 - - - -
305H ALA* 1.3 77.8 - - + +
307H ALA* 1.3 61.8 + - - +
309H ASN* 3.2 23.6 + - - +
332H LEU* 5.5 2.2 - - + -
409H GLN* 3.2 29.3 + - - +
410H VAL 4.0 6.7 + - - -
411H ALA* 3.9 16.4 - - + +
416H GLU* 3.1 30.9 + - + +
417H ALA* 3.5 16.1 - - - +
420H ALA* 3.5 18.6 - - + -
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Residues in contact with ALA 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304H HIS 3.1 9.8 + - - +
306H LYS* 1.3 75.6 - - - +
308H ILE* 1.3 67.5 + - - +
310H ALA* 3.1 19.8 + - - +
311H LEU* 3.8 9.4 - - - +
420H ALA* 3.6 5.4 - - - +
421H LEU* 3.8 35.2 - - + +
424H ASP* 3.8 19.0 + - + +
427H PHE* 4.0 17.0 - - + -
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Residues in contact with ILE 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301H VAL* 3.9 21.1 - - + +
304H HIS 2.9 18.9 + - - +
305H ALA* 2.8 8.8 + - - +
307H ALA* 1.3 75.8 - - - +
309H ASN* 1.3 57.3 + - - +
311H LEU* 2.8 27.0 + - + +
312H ALA* 2.8 19.3 + - + -
360H PHE* 4.1 13.0 - - + -
370H CYS 4.9 0.9 - - - +
373H ALA* 4.1 21.3 - - + +
374H LEU* 3.5 36.1 - - + -
377H ALA* 3.6 28.7 - - + -
427H PHE* 4.4 6.7 - - + -
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Residues in contact with ASN 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305H ALA 2.8 11.3 + - - +
306H LYS* 3.2 18.1 - - - +
308H ILE* 1.3 77.5 - - - +
310H ALA* 1.3 57.6 + - - +
313H ASN* 2.7 58.5 + - - +
319H TYR* 3.7 17.3 - - - +
322H LEU* 4.7 1.2 - - - +
360H PHE* 3.4 20.6 - - - -
410H VAL* 3.4 14.2 - - - +
411H ALA* 2.7 33.0 + - + +
417H ALA* 3.8 4.5 - - + -
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Residues in contact with ALA 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307H ALA 3.1 14.8 + - - +
309H ASN* 1.3 77.8 - - - +
311H LEU* 1.3 49.7 + - - +
313H ASN 4.7 1.8 - - - -
314H PRO* 3.7 9.7 - - - +
414H LEU* 5.0 1.6 - - - -
417H ALA* 3.4 33.6 - - - +
418H LEU* 4.1 13.7 - - + +
421H LEU* 3.8 23.6 - - + -
442H TYR* 2.6 30.7 + - - -
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Residues in contact with LEU 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307H ALA 3.8 16.2 - - - +
308H ILE* 2.8 7.2 + - - +
310H ALA* 1.3 79.6 - - + +
312H ALA* 1.3 58.4 + - - +
313H ASN 3.4 1.5 + - - -
314H PRO* 3.8 4.9 - - - +
365H ALA* 3.2 22.5 - - - +
366H ASN* 4.0 4.3 + - - +
369H LEU* 3.5 31.4 - - + +
370H CYS* 3.7 21.0 - - - +
373H ALA* 3.7 24.2 - - + -
421H LEU* 4.3 17.7 - - + -
428H LEU* 4.9 4.5 - - + -
434H PHE* 4.9 11.2 - - + -
442H TYR* 3.7 27.5 + - + -
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Residues in contact with ALA 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308H ILE* 2.8 20.0 + - + +
311H LEU* 1.3 72.6 - - - +
313H ASN* 1.3 68.3 + - - +
314H PRO* 3.4 4.1 - - - +
360H PHE* 4.1 5.4 - - + -
361H PRO* 3.4 31.6 - - + -
362H ASP* 3.0 29.1 + - - +
365H ALA* 3.5 7.7 - - - +
370H CYS* 3.5 18.4 - - - -
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Residues in contact with ASN 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309H ASN* 2.7 40.3 + - - +
312H ALA* 1.3 82.6 + - - +
314H PRO* 1.3 57.9 - - - +
315H THR 3.3 5.1 + - - -
318H SER* 3.6 16.8 - - - -
319H TYR* 2.8 39.2 + - + +
321H ARG* 4.1 0.3 + - - -
322H LEU* 3.3 19.4 - - + +
360H PHE* 2.7 36.6 - - - +
362H ASP* 3.3 11.6 - - - +
414H LEU* 4.0 1.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il